


Error in Programming

by GirlGamer0



Category: Agents of S.H.I.E.L.D. (TV), Marvel Cinematic Universe
Genre: Alternate Universe, Alternate Universe - Canon Divergence, Brainwashing, Dubious Consent, Evil! Jemma, Extremely Dubious Consent, F/F, Friends to Lovers, Hydra, Hydra! Jemma, Lesbian Character, Lesbian Sex, Lesbian Skye | Daisy Johnson, Mildly Dubious Consent, Mind Control, Ophelia and AIDA are one and the same, Possessed, Psychological Torture, SHIELD, lesbian jemma simmons
Language: English
Status: In-Progress
Published: 2019-03-09
Updated: 2019-03-09
Packaged: 2019-11-14 11:43:32
Rating: Explicit
Warnings: Graphic Depictions Of Violence, Rape/Non-Con
Chapters: 3
Words: 3,542
Publisher: archiveofourown.org
Story URL: https://archiveofourown.org/works/18051893
Author URL: https://archiveofourown.org/users/GirlGamer0/pseuds/GirlGamer0
Summary: As the SHIELD team goes into the Framework, they are separated from one another in not only space but time. Jemma meets a beautiful woman at the Academy. Daisy is working in an office at Hydra. May is a high level Hydra operative. Fits and Coulson’s whereabouts are unknown.The beautiful woman has a plan to escape this program, but needs to fix some errors with the help of Jemma and Daisy, regardless of whether or not they consent.





	1. Into the Framework: Strange Beginnings

****Jemma POV****

Entering the framework was meant to be a quick, simple mission. Get in, eliminate Madame Hydra, get out. But when Jemma Simmons awoke, she found herself back at the SHIELD academy. More importantly, she found herself sharing a dorm with a beautiful woman. Something seemed strange. Jemma, as far as she can remember, had never looked at a woman this way before. Was the mission all a Dream?

In her confusion she doesn’t hear the woman ask her a question. “Hello?! Earth to Jemma?!” She snaps her fingers in front of Jemma’s face. “I asked if you were going to stare at me all day or if you were going to go to Orientation?” The woman giggles, looking fairly bashful. Jemma stents up off the bed.

"I'm sorry Ophelia, I just...." Jemma struggled to come up with an explanation for why she was staring. The usual genius was seemingly empty-headed. Ophelia put her hand on Jemma's shoulder, and as if an idea just popped into her hear, Jemma answers in her beautiful British accent, "I was just taking in your beauty Ophelia. Something about you always seems to captivate me." She blushes before grabbing her bag and heading to Orientation. Ophelia motions that she'll be along soon.

****AIDA POV****

Once the dorm room door is shut she laughs. "This is going to be easier than I thought." Ophelia, or rather AIDA says. In the Framework, she controls reality. A simple touch to a person, even someone's subconscious that has entered her world, she can reprogram their mind. Gaining the BioChemist's trust was easy. Slowly making her fall in love so she would never so much as think of betraying AIDA, that was priceless.

Ophelia struts out of the room to Orientation. She takes a seat next to Jemma. All of the new prospective SHIELD agents have been living on campus for a few days now. In that time, AIDA's virtually erased all memory that Jemma had had about the real world. A few manipulations here and there, Jemma's main desire is to prove that she is worthy of her parents love, that they had abandoned her. During Orientation, Ophelia puts her hand on Jemma's.

Slowly, she manipulates the thoughts that her most valuable asset has. She makes Jemma skeptical of SHIELD's plans, makes her wonder if there is something better than SHIELD. She also slides in a desire to research and invent new devices, ones that will eventually be used to control and manipulate inHumans, not that Jemma will know that, for now.

********A few semesters later******

****Jemma POV****

Jemma is walking through campus with two massive books and several folders of research. In her brisk walk, she doesn't see Ophelia when she rounds a corner. Jemma fumbles around with her books as Ophelia plops backwards. When Jemma realizes what happened she stammers, "Oh my god. Ophelia, I am SO sorry." She puts her books and research down to help her dorm-mate up. Ophelia is laughing, "It's okay Jemma, I wasn't looking."

Jemma, still flustered, continues apologize. She tries to explain her research, "Look, I've been working on the molecular level of...." Ophelia puts her hand on Jemma's folder and a wave on relaxation comes over Jemma. Ophelia smiles, "It's okay, I'll see you back in the dorm room in a few." Jemma nods, and heads back to the dorm room.

It isn't until Jemma gets back into the dorm room and puts the textbooks down that she realizes that one of the two massive books isn't hers. She reads the title, 'Understanding Advanced Neurology.' Curious, Jemma opens the book to a random page. 'Chapter 6: How the Human Brain and a Computer Are One and the Same.' Most prospective agents would do more digging. Hell, even the old Jemma Simmons would have. But, this Jemma, that has spent the past 3 years with Ophelia is enraptured. Her heart practically skips a beat as she thinks that Ophelia is just as dedicated to research as she is.

Jemma closes the book just as Ophelia opens the door. "Ophelia, this is... extremely advanced research." She turns around, head down, clearly blushing. Jemma walks to her bed, sitting down. She looks longingly at Ophelia, biting her lip. Motioning for Ophelia to join her, which she obliges. "Ophelia..... can I do something?"

Ophelia turns her head, her face showing curiosity although her she knows what Jemma is about to do. Jemma brushes some of the black hair away from Ophelia's face before leaning in and kissing her. Although, the kiss comes with both new feelings and consequences. Having such and open portal into Jemma's mind, AIDA takes full advantage.

Any noble notion that Jemma has had is shattered. She is not simply a prospective SHIELD agent. She is a HYDRA sleeper agent. And Ophelia, or rather as she prefers in private, for now, AIDA is Madame Hydra, Jemma's boss and lover. AIDA breaks the kiss. What seemed like a lifetime in reality took less than a minute. AIDA whispers, "Hail Hydra." Jemma answers with a beaming grin, "Hail Hydra."

AIDA leans in and kisses Jemma once more, but with much more passion. She pulls Jemma down, taking her blouse off. Looking up at her lover, Jemma gives a lustful look. Although she would lover to return the favor, Jemma knows that she would be punished for disobeying Madame Hydra's words. Jemma giggles as AIDA rips her belt off. She spreads her legs as if this is a regular tradition, which in Jemma's brainwashed head, this is a regular before bed tradition.

AIDA bends down and pulls Jemma's Hydra-green panties down. Jemma watches as she then lowers her head and slides her tongue inside. Jemma moans while having no idea that AIDA uses this 'tradition' to reinforce Jemma's loyalty to her, both inside the Framework and in the real work.

Jemma can feel AIDA curling, swirling, and wiggling her tongue inside her. She covers her mouth as best as she can to stifle her moans. With her free hand, she rubs and cups her breasts. A sensation quickly moves down Jemma's guts. She screams through her hand as she orgasms at the exact time that AIDA influenced her body to do so. AIDA spends as little time as she has to, for now, pleasuring her 'girlfriend,' as she practices for the real world.

****Hydra Rises****

****AIDA POV****

It's Graduation Day at SHIELD and the entire leadership is in one place for the only time each and every year. Inside the Dorm of Jemma and AIDA however, a discussion is taking place. AIDA dyed a Hydra-green streak in her hair the night before.

"Jemma, today, we come out of the shadows. Today is the day the world shall Hail Hydra. Stay with me and you will not be harmed." AIDA says in a very noble tone. Jemma stands up from the head, She steps forwards in high heels and a Hydra-green skirt. Dressed completely unlike the sweet BioChemist that enters the SHIELD Campus six years prior, Jemma looks much more like an evil, mad-with-power Hydra Scientist. AIDA smiles sweetly as Jemma takes her hand. 

Jemma says, "Of course darling. I would do anything for you. From furthering the cause of Hydra to betraying my 'closest friends.' You're love is all that matters to me." To AIDA, this is music to her ears. She leans in and kisses her loyal girlfriend. Before the duo even leave the dorm room, the sounds of the first gun shots echo down the hallway. The year is 2012.

*****Elsewhere*****

*Skye POV*

Skye awakens from a deep sleep in a cold sweat. Walking out of her bedroom, she's confused to see 'Medal of Valor for Capturing InHumands': Hydra Agent Daisy Johnson' hanging on the wall. The last thing she remembered was telling Jemma that she loved her before entering the Framework in 2016.

*****To Be Continued****


	2. Into the Framework: Waking Up to a Nightmare

**Summary for the Chapter:**

> The last Chapter was the introduction, brainwashing, and corruption of Jemma Simmons in the framework. Five years later, Daisy Johnson awakens to her personal nightmare.

***** Skye POV *****

February 22nd, 2017, Skye awakens in a cold sweat. Her consciousness has finally entered the Framework. She sits up and turns the bedroom light on. She thinks to herself, we all entered together, why are we separated? 

Walking out of the bedroom and down the hall, she notices award after award. Stopping to look at one it reads, ‘Medal of Valor: Awarded to Hydra Agent Daisy Johnson for courage against InHumans.’ “What the hell?” Skye says as she rubs her head. Turning and looking towards her computer she walks over, booting it up.

The Hydra logo appears on the boot-up screen before disappearing. A password request pops up on the screen. Unsure of what her Framework self would have used, she tries a few guesses. ‘InHumansmustdie,’ ‘shieldmustdie,’ and ‘IloveJemma,’ all return with access denied.

Looking back at the award that she is still holding, it says it was awarded by ‘Madame Hydra’s Wife and No. 2 in command,’ ‘The BioChemist.’ Glancing back at the computer, her lips curled, she hesitantly types in, ‘ILoveTheBioChemist.’ The computer boots up.

“What the hell is going on? First I’m a ‘Hydra’ Agent,” Skye says with disgust. “And Jemma is married to Madame Hydra?! That’s one hell of a cover.” She says with a shaky confidence. Who’s to say that this BioChemist is even Jemma? She thinks to herself.

Looking at the desktop screen, she looks for where to do research first. Thinking that she can get up to speed quicker using the Framework’s internet, she clicks on the equivalent to Hydra’s Google Chrome.

It browser automatically goes to the ‘Compliance Network.’ Sunail Bahkshi is pictured as the channel’s anchor. Skye begins to realize that in the Framework, history is different. Bahkshi died years ago in the real world.

The top story is ‘5th Anniversary of the Destruction of Shield.’ Clocking on the story, Skye covers her mouth to muffle her scream. The picture at the top of the story is Madame Hydra and Jemma executing Director Fury and Agent Maria Hill.

Skimming through the article she learns that Madame Hydra and Jemma led the uprising at SHIELD. The next line surprises her, “Jemma ‘The BioChemist’ Simmons wearing her signature Hydra-green skirt, black pumps, and a Hydra-green tube top personally insisted that all SHIELD personnel be executed in the first Hydra purge.”

Skye blinks in disbelief. Thinking to herself, ‘Jemma would never wear anything like that, what the hell was her Framework-self doing.’ Still believing that Jemma entered the Framework at the same time that she did, Skye shutters at the thought of the danger that she believes her girlfriend is in.

Skye’s phone sounds. Shutting the alarm off, she looks at the schedules. ‘5:30 am wake-up.’ ‘8:15 am meeting at HQ.’ ‘8:45 mission briefing with May, use new weapon excuse to meet with ‘The BioChemist <3.’

“Perfect, I’ll use that to get to Jemma! And I can check on May.”

***** Jemma POV *****

Jemma walks out of the bathroom, completely naked. She struts over to her wife, wrapping her arms around her. Madame Hydra blushes and smile, turning to her brainwashed lovesick evil genious of a wife. Her smile fades as she senses Skye’s consciousness enter the program.

Jemma takes a step back as she feels her wife tense up, “Ophelia darling? What’s wrong?” Madame Hydra shoots her a look. The name Ophelia is only reserved to be used by Jemma.

“It’s time I be honest with you.” Madame Hydra walks to the bed and sits down. “This is not the real world. There is an outside world, where you came from. Where I came from. And others hidden in plain sight.” Jemma, laughs. The evil genius struts over to her wife exclaiming, “That’s not possible.”

Madame Hydra turns and looks at her beautiful wife. “It is. My body was nearly destroyed by SHIELD in the real world. There they have been exterminating us. You uploaded my consciousness here, as well as your own at my direction, to preserve Hydra.” 

Pulling Jemma down on top of her, she kisses her. Jemma flatly says in her British accent, “You’re doing it again.” Madame Hydra admitted her powers to Jemma before their marriage, however never mentions that she used it to brainwash her.

“Jemma. As my wife in the real world, you were the only one I could trust. You were the only person that would believe me. With my damaged body, my consciousness needs to be downloaded into someone else, an empty vessel.” Jemma puts her head down. A dark realization setting in.

“That’s what my research has been for. To save you.” Jemma says, tears streaming down her face. She passionately kisses her wife. Before the two can get serious, Jemma’s phone rings. She answers it to see Agent Melinda May. Another victim of Madame Hydra’s brainwashing, May ignores the fact that Jemma is naked and says, “We have a problem. A SHIELD agent, ‘Skye,’ arrived.”

Jemma goes to protest but can feel her wife enter her mind. Madame Hydra speaks to her, ‘May was sent here to kill me. I knocked out her real world consciousness while in my realm. The SHIELD Agent she captured might be a perfect candidate to create an empty vessel for.’

Jemma gives May a deviously evil grin. “Keep her in the hold. We’ll be there when we are ready.” She ends the call before turning to her wife. “Let’s have some fun before we prepare you for your next body.”

Jemma passionately and hungrily kisses AIDA. She rolls AIDA to be on top, the position she believes her wife deserves. AIDA of course, goes through the same process that she has once before, but with a twist. She implants images of Skye inside of Jemma’s Head. She also labels it, ‘Dream hostess of Ophelia.’ AIDA only knows this because the Framework being made by her consciousness, she knows all who are there.

AIDA swirls, curls, and wiggles her tongue inside of Jemma. However, this time, knowing that for once, she may be free of this virtual world, she savors the taste, allowing Jemma to reach an orgasm naturally. Instead of the usual handful of minutes of sex, the two women make love for nearly an hour. AIDA even allows Jemma to eat her out, preparing herself for the real thing.

Afterwards, as the women get dressed for the ‘interrogation,’ AIDA speaks darkly, “Why don’t you wear what you had on when we first met. It might be fun to play head games with a former colleague of yours.” A wickedly evil grin spread across Jemma’s face as she pulls the Shield Agent Prospect class uniform out from deep within the closet.

What AIDA hasn’t said is the powers that Skye has in the real world. The only reason for Jemma’s research isn’t to transfer consciousness from one body to another, but rather powers. Mind control, technology control, teleportation, are all powers that AIDA would like to have, in addition to quake.

***** To Be Continued *****


	3. Inside the Framework: AIDA Rules

**Summary for the Chapter:**

> Skye is captured while trying to warn May. She then comes face to face with both Jemma and AIDA.

**Notes for the Chapter:**

> I am writing this story a little out of order on purpose. This way the events at the end line up.

***** Skye POV *****

With the first meeting at Hydra done, Skye goes to get her mission briefing from May. Thinking that May is at the very least in the same predicament she is in, she plans everything out. Walking into the room, she is almost caught off guard that May is dressed like a Hydra storm trooper. She does her best not to draw attention to themselves as she closes the door.

“May thank god your here. I thought I was on my own.” Skye exhales without a second thought.

May raises an eyebrow. She starts a recorder and asks, “First, only Madame Hydra has the privilege of calling me ‘May.’ Second, Hydra agents are always on there own. Trust is for the weak.” 

Skye listens to May’s diatribe before sitting down and laughing. “Hello, Earth to May, it’s me, Skye. You can drop the act now....” She sees May cross her arms and she looks around. “They’re recording is, aren’t they?”

May closed the mission briefing folder and stands beside Skye. Intrigued, she questions the agent, “Who exactly are you referring to Agent Johnson?”

Skye’s voice begins to tremble as her nerves show through, “Hydra. They must have all of these rooms bugged.” Skye looks around. She raises her hands as if to destroy any cameras or sensors with her Quake abilities but nothing happens. 

May let’s Skye do this a couple of times before turning the mission briefing into an interrogation. “What exactly are you trying to do Agent Johnson? Are you secretly an InHuman, enemy of the American people, of Hydra?” She slams her hand against the desk in front of Skye. “Who sent you?!”

Skye blurts out, hoping the real May is somewhere inside of the Framework version, “SHIELD Director Coulson sent us in her. You, me, Simmons, Fitz!” May smirks before pressing a ‘panic’ button beneath the table. Metal casings lock Skye’s arms and legs into the chair. May steps out of the room to video call Madame Hydra as Skye screams her lungs out in the interrogation room.

******* Several Hours Later *******

*****Jemma POV*****

A Hydra-Green Cadillac Limo pulls up to the Hydra HQ. Jemma steps out before helping AIDA. The two women walk hand-in-hand into the building. Upon entering, Jemma simply says, “Where is she?”

Several agents scramble, not wanting to become her next experiment. Jemma laughs maniacally before leaning in and whispering to AIDA, “I absolutely love seeing the headless chickens run about.” AIDA laughs as the quirky ‘chickens with their heads cutoff’ reference.

May walks up from a nearby stairwell. Madame Hydra, BioChemist, follow me. May leads the women into an elevator. Plunging deep into the bowels of the building they arrive at the prison floor. Jemma reaches over and cuts power to the elevator before it can open, catching May off guard.

Looking at her for an explanation, Jemma laughs. “I’d like to conduct a psychological experiment. Handcuff me and treat me like a prisoner. Sure I can get this.... Daisy Johnson to talk.” Jemma places her arms behind her back, grinning wildly as May handcuffs her. This version of her that AIDA created absolutely loves to torture her prisoners.

The elevator doors finally open and May kicks Jemma out of the elevator. “SHIELD SCUM, move it!” May shouts. AIDA meanwhile stands in the shadows, watching, waiting. Eventually, May shoves Jemma into the same cell as Skye, who catches Jemma in her arms.

“Jemma, oh my god are you okay?” Skye asks, tears streaming down her face. She hugs Jemma once more before kissing her cheek. Jemma blushes as she makes a mental note of how perfect Skye’s body would be for AIDA.

“I’m fine, just in shock. The simulation had me pretend to be Madame Hydra’s wife, for months!” She eyes Skye up and down. “We entered together, do you have any idea why we were separated?”

She watches Skye’s expression. A puzzled look forms on her face. “We didn’t enter exactly at the same time. You went first, then May, myself....” Jemma smirks as she sees AIDA slip into the cell with them.

“Anyway, I had to do so many atrocities. Thank god it’s just a simulation. I have to admit, it was kind of fun knowing that what happens here doesn’t have real world consequences.” While she continues to talk to Skye, Jemma discreetly unlocks her handcuffs.

Jemma stands up, looking down at Skye. “I thought I was going to start forgetting you and embrace life as Ophelia’s wife.” 

Skye laughs loudly. But her laughter slowly tapers. “Ophelia...” Jemma watches Skye’s eyes dart up to her. “Just how close did you two get?” Skye’s eyes narrow.

Jemma laughs and reveals that she is no longer handcuffed. “Oh, she and I are very close. In fact, I ordered the execution of Fury and Hill as a wedding gift.” The tone of Jemma’s voice is twisted, dark, and sadistic. Skye goes to back away, backing into AIDA. 

Skye shouts and jumps into Jemma’s arms. “Miss Johnson, you have quiet the honor.” Jemma forces Skye to watch as AIDA whips out a green-collar like device. “Once my wife places that collar on you, she will be able to replace your consciousness with an exact copy of her own. Then, together, we shall return to the real world and put Hydra in it’s rightful place in the sun!”

Jemma keeps her grip firm on Skye as AIDA places the collar on her. After a few minutes, Skye laughs, much to the amusement of Jemma. “Looks like your brainwashing device didn’t work. Now, if you’ll excuse....”

Skye is interrupted as AIDA pulls her closer. She leans down and gives Skye a passionate kiss. Jemma laughs maniacally as Skye’s eyes go wide. Inside of Skye’s head she can feel every memory, personality trait, and desire be replaced with AIDA’s one by one. 

When AIDA breaks the kiss, she backs away. Skye meanwhile turns to Jemma, her eyes now a Hydra-green. Jemma takes Skye’s hand and says, “test out your powers.” With just a thought the two women are teleported to Madame Hydra’s mansion. 

Skye struts into a room that even Jemma still did not know about. “Honey, what room is this.” AIDA-Skye turns with a seductive grin, “This is how we escape to the real world.”

***** To Be Continued *****


End file.
